Work

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches

Year: 2006

Type: article

Abstract: Protein sequence database search programs may be evaluated both for their retrieval accuracy--the ability to separate meaningful from chance similarities--and for the accuracy of their statistical assessments of reported alignments. However, methods for improving statistical accuracy can degrade retrieval accuracy by discarding compositional evidence of sequence relatedness. This evidence may be preserved by combining essentially independent measures of alignment and compositional similarity into a unified measure of sequence similarity. A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkl731

Authors: Yi-Kuo Yu, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer, Stephen F. Altschul

Institutions: National Institutes of Health, National Center for Biotechnology Information

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funders: U.S. Department of Health and Human Services, National Institutes of Health, U.S. National Library of Medicine